My best guess, and I'm venturing into pure speculation here: Kris is missing their soul somehow. To seal the dark fountains, possibly in an effort to save Dess, they need a human soul. Only Kris can contain the soul; they're the only human in town. So they've called another human soul into their body, and that soul happens to be mine. (Or yours! It's the player's soul, in any case.) We're not controlling Kris's soul; we're an entirely separate soul, and Kris's soul is absent.

That makes a creepy amount of sense! Kris seems desperate to glue their crumbling life back together, so they turned to powers beyond their own world in hopes of changing fate. And it comes with a steeper price than they imagined. D:

I love Deltarune so much. Every chapter feels like a cliffhanger because I want to know what's going on so badly. ;;